TDP-43 Cryptic RNAs in Perry Syndrome: Differences across Brain Regions and TDP-43 Proteinopathies

Abstract

Background: Perry syndrome (PS) is a rare and fatal hereditary autosomal dominant neurodegenerative disorder caused by mutations in dynactin (DCTN1). PS brains accumulate inclusions positive for ubiquitin, transactive-response DNA-binding protein of 43 kDa (TDP-43), and to a lesser extent dynactin.

Objectives: Little is known regarding the contributions of TDP-43, an RNA binding protein that represses cryptic exon inclusion, in PS. Therefore, we sought to identify the degree of TDP-43 dysfunction in two regions of PS brains.

Methods: We evaluated the levels of insoluble pTDP-43 and TDP-43-regulated cryptic RNAs and protein in the caudate nucleus and substantia nigra of 7 PS cases, 12 cases of frontotemporal lobar degeneration (FTLD) with TDP-43 pathology, and 11 cognitively healthy controls without TDP-43 pathology.

Results: Insoluble pTDP-43 protein levels were detected in PS brains to a similar extent in the caudate nucleus and substantia nigra but lower than those in FTLD brains. The caudate nucleus of PS showed accumulation of eight TDP-43-regulated cryptic RNAs (ACTL6B, CAMK2B, STMN2, UNC13A, KCNQ2, ATG4B, GPSM2, and HDGFL2) and cryptic protein (HDGFL2) characteristic of FTLD. Conversely, only one cryptic target, UNC13A, reached significance in the substantia nigra despite similar pTDP-43 levels.

Conclusion: We detected TDP-43 cryptic RNAs and protein in PS caudate nucleus. Given the importance of cryptic exon biology in the development of biomarkers, and the identification of novel targets for therapeutic intervention, it is imperative we understand the consequences of TDP-43 dysfunction across different brain regions and determine the targets that are specific and common to TDP-43 proteinopathies. © 2025 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Keywords: Perry syndrome; cryptic; frontotemporal dementia; frontotemporal lobar degeneration; transactive‐response DNA‐binding protein of 43 kDa (TDP‐43).

FIG. 1

TDP‐43 (transactive‐response DNA‐binding protein of 43 kDa) pathology accumulates to a similar extent in the caudate nucleus and substantia nigra of PS (Perry syndrome) cases. Immunohistochemical staining of phosphorylated TDP‐43 pathology in PS brains illustrating (A) intranuclear inclusions, (B) dendritic neurites, (C) neuronal cytoplasmic inclusions, (D) glial cytoplasmic inclusions, and (E) axonal spheroids. (F) Levels of pTDP‐43 were measured by immunoassay in the detergent‐insoluble, urea‐soluble fraction extracted from the caudate nucleus and substantia nigra of PS, FTLD, and control (Ctrl) brains. Graph represents mean ± SEM (standard error of the mean). Statistical differences were assessed using nonparametric Kruskal–Wallis test followed by Dunn's multiple comparison test; *P < 0.05, **P < 0.005, ***P < 0.001, and ****P < 0.0001; ns, not significant. [Correction added on 21 February 2025, after first online publication: The figure 1 has been updated.] [Color figure can be viewed at wileyonlinelibrary.com]

FIG. 2

Certain TDP‐43 (transactive‐response DNA‐binding protein of 43 kDa) cryptic (or skiptic) RNAs targets are upregulated in PS (Perry syndrome) caudate nucleus. The levels of (A) neuronal cryptic RNAs and skiptic neuronal RNA, (B) more ubiquitous RNAs, or (C) HDGFL2 cryptic protein were measured from the caudate nucleus and substantia nigra of PS, FTLD, and control (Ctrl) cases. Graphs represent mean ± SEM (standard error of the mean). Statistical differences were assessed using nonparametric Kruskal–Wallis test followed by Dunn's multiple comparison test; *P < 0.05, **P < 0.005, ***P < 0.001, and ****P < 0.0001; ns, not significant. [Color figure can be viewed at wileyonlinelibrary.com]

FIG. 3

Cell‐type composition may explain differential accumulation of cryptic RNAs within certain brain regions but does not explain differences across brain regions. (A) RNA expression values were derived from The Human Protein Atlas for the cell types and transcripts shown. RNA levels of (B) neuronal (RBFOX3), (C) astrocytic (GFAP), (D) oligodendrocytic (OLG2), and (E) microglial (TMEM119) markers were measured using qRT‐PCR. Caud., caudate nucleus; SN, substantia nigra. Graphs represent mean ± SEM (standard error of the mean). Statistical differences were assessed using nonparametric Kruskal–Wallis test followed by Dunn's multiple comparison test; *P < 0.05, **P < 0.005, ***P < 0.001, and ****P < 0.0001; ns, not significant. [Color figure can be viewed at wileyonlinelibrary.com]